The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities - Supplementary Tables
Creators
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1.
ETH Zurich
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2.
University of Amsterdam
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3.
European Molecular Biology Laboratory
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4.
Leiden University
Description
Supplementary Table 1:
A map between each of the genomes in mOTUs-db (3’747’151), the associated study and its metagenomic sample (in case of MAGs).
Columns:
GENOME → Unique mOTUs-db name of the genome STUDY → Unique mOTUs-db name of the study IS_MAG → True if genome is a MAG, otherwise False METAGENOMIC_SAMPLE → Unique name of the metagenomic sample or NA in case of non-MAG genome
Example:
GENOME STUDY IS_MAG METAGENOMIC_SAMPLE --------------------------------------------------------------------------------------------- ACIN21-1_SAMN05421555_MAG_00000001 ACIN21-1 True ACIN21-1_SAMN05421555_METAG RSGB23-1_GCA-006096615-V1_GENO_10000001 RSGB23-1 False NA
Supplementary Table 2:
A map between all non-MAG genomes (919’090) and their source (e.g. Refseq or JGI).
Columns:
GENOME → Unique mOTUs-db name of the genome SOURCE_SAMPLE_LINK → Link to the original location of this genome
Example:
#GENOME SOURCE_SAMPLE_LINK -------------------------------------------------------------------------------------------------------- JGIG23-1_GA0055041_GENO_10000001 https://gold.jgi.doe.gov/analysis_project?id=Ga0055041 RSGB23-1_GCA-006717865-V1_GENO_10000001 https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_006717865.1
Supplementary Table 3:
A list of all metagenomic studies processed for the mOTUs-db, their number of samples, the number of reconstructed MAGs and the associated publication.
Columns:
STUDY --> Unique mOTUs-db study identifier BIOPROJECT --> Public identifier (NCBI/JGI) of metagenomic sequencing project SAMPLES --> Number of metagenomic samples MAGs --> Number of reconstructed MAGs PUBLICATION --> Link to publication
Example:
STUDY BIOPROJECT SAMPLES MAGs PUBLICATION ------------------------------------------------------------------------------------------------- ACIN21-1 PRJEB44456 58 1,110 https://www.nature.com/articles/s42003-021-02112-2
Supplementary Table 4:
Mapping between mOTUs-db sample identifier, the associated biosample and the environment.
Columns:
SAMPLE --> Unique mOTUS-db sample identifier BIOSAMPLE --> Public identifier (NCBI/JGI) of metagenomic sample STUDY --> Unique mOTUs-db study identifier ENVIRONMENT --> Environment of metagenomic sample SOURCE_SAMPLE_LINK --> Link to the original location of this sample
Example:
#SAMPLE BIOSAMPLE STUDY ENVIRONMENT SOURCE_SAMPLE_LINK --------------------------------------------------------------------------------------------------------------------- ACIN21-1_SAMN05421555_METAG SAMN05421555 ACIN21-1 marine https://www.ncbi.nlm.nih.gov/biosample/SAMN05421555/
Supplementary Table 5:
A list of environments covered in the mOTUs-db mapped to the respective NCBI taxonomy (if possible)
Columns:
TERM --> Unique environment name NCBI TAXONOMY ID --> Link to the NCBI taxonomy
Example:
TERM NCBI TAXONOMY ID ---------------------------------------------- activated sludge metagenome NCBI:txid942017 air metagenome NCBI:txid655179